A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota DOI Creative Commons
Joshua M. Kirsch, Andrew J. Hryckowian, Breck A. Duerkop

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Oct. 9, 2023

Abstract Insertion sequence (IS) elements are mobile genetic in bacterial genomes that support adaptation. We developed a database of IS coupled to computational pipeline identifies element insertions the microbiota. discovered diverse insert into intestinal bacteria regardless human host lifestyle. These target accessory genes aid their adaptation unique environmental conditions. Using expansion Bacteroides , we show activity leads insertion “hot spots” genes. stable and can be transferred between humans. Extreme perturbations force fall out microbiota many fail rebound following homeostasis. Our work shows drive genome diversification within establishes framework for understanding how strain level variation impacts health.

Language: Английский

Quantifying the adaptive landscape of commensal gut bacteria using high-resolution lineage tracking DOI Creative Commons
Daniel P.G.H. Wong, Benjamin H. Good

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 21, 2024

Gut microbiota can adapt to their host environment by rapidly acquiring new mutations. However, the dynamics of this process are difficult characterize in dominant gut species complex vivo environment. Here we show that fine-scale genome-wide transposon libraries enable quantitative inferences these evolutionary forces. By analyzing >400,000 lineages across four human Bacteroides strains gnotobiotic mice, observed positive selection on thousands cryptic variants - most which were unrelated original gene knockouts. The spectrum fitness benefits varied between species, and displayed diverse tradeoffs over time different dietary conditions, enabling underlying function. These results suggest within-host adaptations arise from an intense competition numerous contending variants, strongly influence emergent tradeoffs.

Language: Английский

Citations

8
Epigenetic phase variation in the gut microbiome enhances bacterial adaptation DOI Creative Commons
Mi Ni, Yu Fan, Yujie Liu

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 12, 2025

Abstract The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, enable a single strain exhibit variable phenotypic states. Genome-wide site-specific ePV have been well characterized pathogens’ antigenic virulence factor production. However, role of facilitating remains poorly understood. Here, we comprehensively cataloged genome-wide infant adult microbiomes. First, using long-read metagenomic sequencing, detected complex structural methyltransferases, highlighting ones associated with antibiotics or fecal microbiota transplantation. Second, analyzed an extensive collection public short-read sequencing datasets, uncovering greater prevalence microbiome. Third, quantitatively ePVs single-molecule methylation analysis identify dynamic antibiotic treatment probiotic engraftment. Finally, performed in-depth assessment Akkermansia muciniphila isolate from infant, that expression adaptive capacity employing bet-hedging increase tolerance differing antibiotics. Our findings indicate modifications are common broad used bacteria adapt their environment.

Language: Английский

Citations

0
Do the Shuffle: Expanding the Synthetic Biology Toolkit for Shufflon-like Recombination Systems DOI Creative Commons

Jan Katalinić,

Morgan Richards,

Alex Auyang

et al.

ACS Synthetic Biology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 27, 2025

Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, availability single enzyme with moderate rates recombination hampered more widespread use SIs. We identified 14 previously untested SI genes their sites public databases. established assay based on single-molecule sequencing that allows quantification these enzymes determined cross-recognition to identify orthogonal SI/sfx pairs. describe substantially improved shuffling when expressed inducible manner E. coli. Our findings will facilitate SIs engineering biology where shufflons enable millions sequence variants vivo applications such barcoding or experimental selection.

Language: Английский

Citations

0
100+ years of phase variation: the premier bacterial bet-hedging phenomenon DOI
Christopher D. Bayliss, Jack Clark, Marjan W. van der Woude

et al.

Microbiology, Journal Year: 2025, Volume and Issue: 171(2)

Published: Feb. 27, 2025

Stochastic, reversible switches in the expression of Salmonella flagella variants were first described by Andrewes 1922. Termed phase variation (PV), subsequent research found that this phenomenon was widespread among bacterial species and controlled major determinants bacterial-host interactions. Underlying mechanisms not discovered until 1970s/1980s but to encompass intrinsic aspects DNA processes (i.e. slippage recombination) modifications methylation). Despite long history, discoveries are ongoing with expansions phase-variable repertoire into new organisms novel insights functions known loci switching mechanisms. Some these somewhat controversial as term 'PV' is being applied without addressing key such whether mutations or epigenetic changes generated prior selection. Another 'missing' aspect PV impact adaptive real-world situations. This review provides a perspective on historical timeline discovery PV, current state-of-the-art, classifying possible effects phenomenon.

Language: Английский

Citations

0
Comprehensive profiling of genomic invertons in defined gut microbial community reveals associations with intestinal colonization and surface adhesion DOI Creative Commons
Xiaofan Jin, Alice G. Cheng, Rachael B. Chanin

et al.

Microbiome, Journal Year: 2025, Volume and Issue: 13(1)

Published: March 10, 2025

Language: Английский

Citations

0
Mind the gap: Intergenic regions in bacteria encode numerous small proteins DOI

Jordan D. Lin,

Ami S. Bhatt

Molecular Cell, Journal Year: 2025, Volume and Issue: 85(6), P. 1046 - 1048

Published: March 1, 2025

Language: Английский

Citations

0
A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota DOI
Joshua M. Kirsch, Andrew J. Hryckowian, Breck A. Duerkop

et al.

Cell Host & Microbe, Journal Year: 2024, Volume and Issue: 32(5), P. 739 - 754.e4

Published: April 1, 2024

Language: Английский

Citations

3
Viruses May Be Redefined as Self-Replicating Entities: Expanding the Definition of Life DOI Open Access
George B. Stefano, Pascal Büttiker,

Simon Weissenberger

et al.

THE MIND - Bulletin on Mind-Body Medicine Research, Journal Year: 2024, Volume and Issue: 3

Published: Dec. 12, 2024

Conclusion:A Charité MBM course has shown beneficial effects to reduce perceived negative stress, increase self-awareness, mindfulness and empathy as well promote integrative concepts of doctor-patient relationship.Further research including RCT trials are needed validate the benefits courses for medical students in a larger study population

Language: Английский

Citations

1
Jekyll and Hyde flip of the script when bacteria invert gene sequences DOI

Chia-Chi Chang,

Robert R. Jenq

Nature, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 25, 2024

Language: Английский

Citations

0
Do the shuffle: Expanding the synthetic biology toolkit for shufflon-like recombination systems DOI Creative Commons

Jan Katalinić,

Morgan Richards,

Alex Auyang

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

Abstract Naturally occurring DNA inversion systems play an important role in the generation of genetic variation and adaptation prokaryotes. Shufflon invertase (SI) Rci from plasmid R64, recognizing asymmetric sfx sites, has been adopted as a tool for synthetic biology. However, availability single enzyme with moderate rates recombination hampered more widespread use SIs. We identified 14 previously untested SI genes their sites public databases. established assay based on single-molecule sequencing that allows quantification these enzymes determined cross-recognition to identify orthogonal SI/ pairs. describe substantially improved shuffling when expressed inducible manner E. coli . Our findings will facilitate SIs engineering biology where shufflons enable millions sequence variants vivo applications such barcoding or experimental selection.

Language: Английский

Citations

0